[gmx-users] To make continuous trj in REMD

[Justin A. Lemkul]

Qin Qiao wrote:
> 
> 
> 2011/1/7 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     Qin Qiao wrote:
> 
>         Dear all,
> 
>         I came across a problem when I want to make the REMD
>         trajectories continuous.
> 
>         What I did:
> 
>         1. 'demux.pl <http://demux.pl> <http://demux.pl> REMD_0.log'    
>              --to get the 'replica_index.xvg'
> 
>         2. 'trjcat -f ../REMD_*.xtc -o resort.xtc -demux
>         ../replica_index.xvg'
> 
>         It seems smooth. But when I check the rmsd of the output
>         0_resort.xtc, I found it's still discontinuous.. with big jumps
>         about 0.5nm..! Could you help me to figure out what's wrong?
>         Thanks a lot.
> 
> 
>     Have you properly accounted for periodicity effects?
> 
>     -Justin
> 
> 
> It's the same after I remove periodicity by trjconv -pbc mol -ur compact ...
>  

One iteration of trjconv is not necessarily enough to produce a properly imaged 
trajectory.  What is going on in the trajectory when these spikes are occurring?

-Justin

> 
>         Best,
> 
>         Qin
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================